The objective of this study was to investigate the impacts of
Bacillus subtilis
(
BS
), ATCC 6051a strain, as a probiotic bacterium in broiler diets based of 2 protein sources (soybean meal [
SBM
] and cowpea seeds [
CWP
]), on growth performance (
GP
), carcass traits, bone mineralization, and microflora population (0 to 42 d age). The SBM and CWP starter, grower, and finisher diets were tested in the presence or absence of BS (5.0 × 10
11
CFU spores g
−1
feed) in a 2 × 2 factorial arrangement of treatments in a completely randomized design. Broilers were randomly assigned to 4 dietary treatments with 6 replicate pens per treatment (20 chicks per pen). The results showed that broilers fed CWP had comparable GP (body weight gain, feed intake, and feed conversion ratio) to the birds fed the SBM diet. Carcass, breast and legs' yield, organ size (i.e., gizzard, liver, pancreas, small intestine, cecum), and bone development were not affected by the protein source. The addition of BS in both types of diet improved BWG (
P
< 0.001) and feed efficiency, especially in the grower and finisher period (
P
= 0.047;
P
= 0.043
,
respectively). In addition, BS significantly decreased abdominal fat (
P
= 0.026) and cecum weight (
P
= 0.034) and increased tibia bone P concentration (
P =
0.015). Furthermore, BS decrease cecal pH (
P =
0.010) and reduced
Escherichia coli
and
Staphylococcus
spp. from cecum and excreta broilers (
P
< 0.001;
P
< 0.0001
,
respectively). It is concluded that the BS significantly improved the GP of broilers and can beneficially affect the gut and excreta bacterial community in both SBM and CWP diets.